This is an R Markdown website for a reproducible research workshop at SISMID 2024.

In the short course, we’ll use several packages which are listed below. Code to install the packages follows, and version information about each of these packages and their dependencies is at the bottom of this page.

Installing packages from CRAN

# main packages
install.packages(c("tidyverse"))

# additional packages used for visualization
install.packages(c("viridis", "patchwork"))

Installing packages from GitHub

# install projectr from GitHub
install.packages("devtools")
devtools::install_github("julia-wrobel/projectr")

Versions of key packages:

devtools::session_info(c("tidyverse"))
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.2.0 (2022-04-22)
##  os       macOS Big Sur/Monterey 10.16
##  system   x86_64, darwin17.0
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       America/New_York
##  date     2024-07-15
##  pandoc   2.18 @ /usr/local/bin/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────
##  package       * version date (UTC) lib source
##  askpass         1.1     2019-01-13 [1] CRAN (R 4.2.0)
##  assertthat      0.2.1   2019-03-21 [1] CRAN (R 4.2.0)
##  backports       1.4.1   2021-12-13 [1] CRAN (R 4.2.0)
##  base64enc       0.1-3   2015-07-28 [1] CRAN (R 4.2.0)
##  bit             4.0.4   2020-08-04 [1] CRAN (R 4.2.0)
##  bit64           4.0.5   2020-08-30 [1] CRAN (R 4.2.0)
##  blob            1.2.3   2022-04-10 [1] CRAN (R 4.2.0)
##  broom           1.0.1   2022-08-29 [1] CRAN (R 4.2.0)
##  bslib           0.4.2   2022-12-16 [1] CRAN (R 4.2.0)
##  cachem          1.0.6   2021-08-19 [1] CRAN (R 4.2.0)
##  callr           3.7.2   2022-08-22 [1] CRAN (R 4.2.0)
##  cellranger      1.1.0   2016-07-27 [1] CRAN (R 4.2.0)
##  cli             3.5.0   2022-12-20 [1] CRAN (R 4.2.0)
##  clipr           0.8.0   2022-02-22 [1] CRAN (R 4.2.0)
##  colorspace      2.0-3   2022-02-21 [1] CRAN (R 4.2.0)
##  cpp11           0.4.7   2023-12-02 [1] CRAN (R 4.2.0)
##  crayon          1.5.2   2022-09-29 [1] CRAN (R 4.2.0)
##  curl            4.3.2   2021-06-23 [1] CRAN (R 4.2.0)
##  data.table      1.14.6  2022-11-16 [1] CRAN (R 4.2.0)
##  DBI             1.1.3   2022-06-18 [1] CRAN (R 4.2.0)
##  dbplyr          2.2.1   2022-06-27 [1] CRAN (R 4.2.0)
##  digest          0.6.31  2022-12-11 [1] CRAN (R 4.2.0)
##  dplyr           1.0.10  2022-09-01 [1] CRAN (R 4.2.0)
##  dtplyr          1.2.2   2022-08-20 [1] CRAN (R 4.2.0)
##  ellipsis        0.3.2   2021-04-29 [1] CRAN (R 4.2.0)
##  evaluate        0.19    2022-12-13 [1] CRAN (R 4.2.0)
##  fansi           1.0.3   2022-03-24 [1] CRAN (R 4.2.0)
##  farver          2.1.1   2022-07-06 [1] CRAN (R 4.2.0)
##  fastmap         1.1.0   2021-01-25 [1] CRAN (R 4.2.0)
##  forcats         0.5.2   2022-08-19 [1] CRAN (R 4.2.0)
##  fs              1.5.2   2021-12-08 [1] CRAN (R 4.2.0)
##  gargle          1.2.0   2021-07-02 [1] CRAN (R 4.2.0)
##  generics        0.1.3   2022-07-05 [1] CRAN (R 4.2.0)
##  ggplot2         3.5.0   2024-02-23 [1] CRAN (R 4.2.0)
##  glue            1.6.2   2022-02-24 [1] CRAN (R 4.2.0)
##  googledrive     2.0.0   2021-07-08 [1] CRAN (R 4.2.0)
##  googlesheets4   1.0.1   2022-08-13 [1] CRAN (R 4.2.0)
##  gtable          0.3.1   2022-09-01 [1] CRAN (R 4.2.0)
##  haven           2.5.1   2022-08-22 [1] CRAN (R 4.2.0)
##  highr           0.9     2021-04-16 [1] CRAN (R 4.2.0)
##  hms             1.1.2   2022-08-19 [1] CRAN (R 4.2.0)
##  htmltools       0.5.4   2022-12-07 [1] CRAN (R 4.2.0)
##  httr            1.4.4   2022-08-17 [1] CRAN (R 4.2.0)
##  ids             1.0.1   2017-05-31 [1] CRAN (R 4.2.0)
##  isoband         0.2.6   2022-10-06 [1] CRAN (R 4.2.0)
##  jquerylib       0.1.4   2021-04-26 [1] CRAN (R 4.2.0)
##  jsonlite        1.8.4   2022-12-06 [1] CRAN (R 4.2.0)
##  knitr           1.41    2022-11-18 [1] CRAN (R 4.2.0)
##  labeling        0.4.2   2020-10-20 [1] CRAN (R 4.2.0)
##  lattice         0.20-45 2021-09-22 [2] CRAN (R 4.2.0)
##  lifecycle       1.0.3   2022-10-07 [1] CRAN (R 4.2.0)
##  lubridate       1.9.0   2022-11-06 [1] CRAN (R 4.2.0)
##  magrittr        2.0.3   2022-03-30 [1] CRAN (R 4.2.0)
##  MASS            7.3-57  2022-04-22 [1] CRAN (R 4.2.0)
##  Matrix          1.4-1   2022-03-23 [2] CRAN (R 4.2.0)
##  memoise         2.0.1   2021-11-26 [1] CRAN (R 4.2.0)
##  mgcv            1.8-40  2022-03-29 [2] CRAN (R 4.2.0)
##  mime            0.12    2021-09-28 [1] CRAN (R 4.2.0)
##  modelr          0.1.9   2022-08-19 [1] CRAN (R 4.2.0)
##  munsell         0.5.0   2018-06-12 [1] CRAN (R 4.2.0)
##  nlme            3.1-157 2022-03-25 [2] CRAN (R 4.2.0)
##  openssl         2.0.4   2022-10-17 [1] CRAN (R 4.2.0)
##  pillar          1.8.1   2022-08-19 [1] CRAN (R 4.2.0)
##  pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
##  prettyunits     1.1.1   2020-01-24 [1] CRAN (R 4.2.0)
##  processx        3.7.0   2022-07-07 [1] CRAN (R 4.2.0)
##  progress        1.2.2   2019-05-16 [1] CRAN (R 4.2.0)
##  ps              1.7.1   2022-06-18 [1] CRAN (R 4.2.0)
##  purrr           0.3.5   2022-10-06 [1] CRAN (R 4.2.0)
##  R6              2.5.1   2021-08-19 [1] CRAN (R 4.2.0)
##  rappdirs        0.3.3   2021-01-31 [1] CRAN (R 4.2.0)
##  RColorBrewer    1.1-3   2022-04-03 [1] CRAN (R 4.2.0)
##  readr           2.1.2   2022-01-30 [1] CRAN (R 4.2.0)
##  readxl          1.4.1   2022-08-17 [1] CRAN (R 4.2.0)
##  rematch         1.0.1   2016-04-21 [1] CRAN (R 4.2.0)
##  rematch2        2.1.2   2020-05-01 [1] CRAN (R 4.2.0)
##  reprex          2.0.2   2022-08-17 [1] CRAN (R 4.2.0)
##  rlang           1.1.2   2023-11-04 [1] CRAN (R 4.2.0)
##  rmarkdown       2.19    2022-12-15 [1] CRAN (R 4.2.0)
##  rstudioapi      0.14    2022-08-22 [1] CRAN (R 4.2.0)
##  rvest           1.0.3   2022-08-19 [1] CRAN (R 4.2.0)
##  sass            0.4.4   2022-11-24 [1] CRAN (R 4.2.0)
##  scales          1.3.0   2023-11-28 [1] CRAN (R 4.2.0)
##  selectr         0.4-2   2019-11-20 [1] CRAN (R 4.2.0)
##  stringi         1.7.8   2022-07-11 [1] CRAN (R 4.2.0)
##  stringr         1.5.0   2022-12-02 [1] CRAN (R 4.2.0)
##  sys             3.4     2020-07-23 [1] CRAN (R 4.2.0)
##  tibble          3.1.8   2022-07-22 [1] CRAN (R 4.2.0)
##  tidyr           1.2.1   2022-09-08 [1] CRAN (R 4.2.0)
##  tidyselect      1.2.0   2022-10-10 [1] CRAN (R 4.2.0)
##  tidyverse       1.3.2   2022-07-18 [1] CRAN (R 4.2.0)
##  timechange      0.1.1   2022-11-04 [1] CRAN (R 4.2.0)
##  tinytex         0.43    2022-12-13 [1] CRAN (R 4.2.0)
##  tzdb            0.3.0   2022-03-28 [1] CRAN (R 4.2.0)
##  utf8            1.2.2   2021-07-24 [1] CRAN (R 4.2.0)
##  uuid            1.1-0   2022-04-19 [1] CRAN (R 4.2.0)
##  vctrs           0.5.1   2022-11-16 [1] CRAN (R 4.2.0)
##  viridisLite     0.4.1   2022-08-22 [1] CRAN (R 4.2.0)
##  vroom           1.5.7   2021-11-30 [1] CRAN (R 4.2.0)
##  withr           2.5.0   2022-03-03 [1] CRAN (R 4.2.0)
##  xfun            0.35    2022-11-16 [1] CRAN (R 4.2.0)
##  xml2            1.3.3   2021-11-30 [1] CRAN (R 4.2.0)
##  yaml            2.3.6   2022-10-18 [1] CRAN (R 4.2.0)
## 
##  [1] /Users/dbenkes/Library/R/x86_64/4.2/library
##  [2] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
## 
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